In metropolitan regions made up of multiple independent jurisdictions, adaptation to increased coastal flooding due to sea level rise requires coordinated strategic planning of the physical and organizational approaches to be adopted. Here, we explore a flexible method for estimating physical adaptation costs along the San Francisco Bay shoreline. Our goal is to identify uncertainties that can hinder cooperation and decision-making. We categorized shoreline data, estimated the height of exceedance for sea level rise scenarios, and developed a set of unit costs for raising current infrastructure to meet future water levels. Using these cost estimates, we explored critical strategic planning questions, including shoreline positions, design heights, and infrastructure types. For shoreline position, we found that while the shortest line is in fact the least costly, building the future shoreline at today’s transition from saltwater to freshwater vegetation is similar in cost but allows for the added possibility of conserving saltwater wetlands. Regulations requiring a specific infrastructure design height above the water level had a large impact on physical construction costs, increasing them by as much as 200%. Finally, our results show that the costs of raising existing walls may represent 70% to 90% of the total regional costs, suggesting that a shift to earthen terraces and levees will reduce adaptation costs significantly.